已经完成基因组测序或正在进行基因组测序的陆生植物及其基因组大小（1pg等于978Mb）

 

1.         拟南芥Arabidopsis thaliana (thale cress) (114.5 Mb/125 Mb total) has been sequenced in the year 2000  5 Chr.

2.         水稻 rice Oryza sativa 389Mbp  430mb 12 Chr.   Indica 466Mb 12n

3.         大麦barley 5439 Mbp

4.         小麦 wheat Triticum aestivum ABD*7=21条染色体 六倍体面包小麦ABD 2n=6X=42 16979 Mb  硬粒小麦12030Mb    一粒小麦 5700 Mb 二倍体Aegilops tauschii （D基因组来源）is a wild plant species that is diploid (2n = 14) with genome size about 4000 Mb. Triticum aestivum is the product of hybridization between Triticum turgidum (AABB) and Ae. tauschii (DD)

5.         燕麦Avena sativa (oat) 2n = 6x = 42) oat species with a genome of about 11000 Mbp

6.         玉米  maize Zea mays 2365Mbp 10Chr.

7.         高梁sorghum bicolor 760 Mbp 10Chr.

8.         二穗短柄草Brachypodium distachyon(common name purple false brome 紫色假燕麦)2n=2x=10 164Mb model cereal, biofuel

9.         谷子foxtail millet 栗，小米，狗尾栗 Setaria italica 515 Mb 9 chromosomes: I, II, III, IV, V, VI, VII, VIII, IX 遗传图谱Devos_98

10.     杨树 poplar tree populus trichocarpa 480mb 19n

11.     葡萄 graperine vitis vinifera 19 Chr. 500 Mb 2n = 38

12.     蕃木瓜 papaya Carica papaya 9Chr. 372 Mb

13.     马铃薯potato 850 Mbp 12 Chr. Solanum tuberosum L

14.     烟草 N. tabacum is an amphiploid species (2n=48) likely resulting from an interspecific cross between N. sylvestris (2n=24) and N. tomentosiformis (2n=24), and at approximately 4.5 billion base pairs

15.     苜蓿 medicago Medicago Truncatula 500mb 8n

16.     大豆soybean  20 chromosomes unknown chromosome size

17.     百脉根(Lotus japonicus)MG-20  472  6n  Weed legume with a small genome

18.     番茄 tomato Solanum lycopersicum 950 Mb 12n

19.     松树 pine

20.     洋葱 onion Allium cepa  15000 Mb distributed over 8 large chromosomes

21.     芹菜Apium graveolens (celery) 11 chromosomes

22.     石卷柏Asparagus officinalis (garden asparagus) 10 chromosomes

23.     香蕉banana

24.     白菜Brassica oleracea甘蓝 B. rapa白菜 B. nupus 油菜an allotetraploid (AACC genome type, 2n = 38).

25.     芥菜Brassica juncea (Indian mustard) polyploid having AABB genome type and 18 haploid chromosomes

26.     蓖麻Castor bean  Ricinus communis ~400 Mbp 10n

27.     Chlamydomonas reinhardtii 100Mb 17n

28.     蓝桉Eucalyptus globulus  600Mb 11n

29.     Ostreococcus lucimarinus CCE9901  13.25mb 21 n

30.     Ostreococcus tauri OTH95 12.5mb 20n

31.     Physcomitrella patens subsp. patens 511mb 27n

32.     木薯Manihot esculenta (cassava)  760-770 Mb with 18 haploid chromosomes Root crop that grows in the tropical and subtropical regions of the world

33.     甜菜Beta vulgaris (beet) 758 Mb 2N=18

34.     茶Camellia sinensis (tea) 15 chromosomes

35.     胡椒Capsicum annuum (pepper) 2,700 Mbp with 2n=24 chromosomes

36.     柚子Citrus maxima (pomelo orange) 9 chromosomes

37.     榛子Corylus avellana (hazelnut) 11 chromosomes

38.     胡萝卜Daucus carota (carrot)

39.     穇子Eleusine coracana (finger millet) 18 chromosomes an allotetraploid (2n = 4x = 40) cereal

40.     Eragrostis tef (tef) 20 chromosomes  C-4 metabolism

41.     牛毛草Festuca pratensis (meadow fescue) 7 chromosomes

 

EST: expressed sequence tags

GSS:genome survey sequence

HTG:high throughput genomic sequence

WGS:

PLN

 

 http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi?p3=11:Plants&taxgroup=11:Plants|12%3A

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

谷子

Principal Investigators: J.L. Bennetzen, K.M. Devos, A.N. Doust, E.A. Kellogg, D. Ware, and J. Zale

Foxtail millet (Setaria italica) is a diploid grass with a relatively small genome (~515 Mb). It is an important grain crop in temperate, subtropical, and tropical Asia and in parts of southern Europe, and is grown for forage in North America, South America, Australia, and North Africa. The genetic map of foxtail millet is highly colinear with that of rice, despite the fact that these lineages last shared a common ancestor more than 50 million years ago. Hence, comparison of the rice and foxtail millet genomes will facilitate reconstruction of the ancestral grass genome. Most important, foxtail millet is a close relative of an important biofuel crop, switchgrass (Panicum virgatum). It is also closely related to pearl millet (Pennisetum glaucum), which is under investigation as a biofuel grain feedstock in regions unsuitable for maize cultivation, and napiergrass (Pennisetum purpureum), a grass with biofuel potential in hot/humid regions such as the southeastern United States. Switchgrass is a polyploid species with a large genome that will not be an easy target for full genome sequence analysis. However, switchgrass and foxtail millet are both temperate, C4 grass species (C3 and C4 represent different metabolic approaches to CO2 metabolism in plants), so foxtail millet should share many genetic and physiological processes with switchgrass. Hence, foxtail millet should serve as an excellent surrogate genome to assist future study and improvement of switchgrass and related biofuel crops.

耧斗菜

A central goal of biology is to understand the natural genetic variation that is responsible for environmental adaptations, leading to species and higher-order taxa. In order to understand the key features of angiosperm (flowering plant) evolution, we need genomic resources for model organisms from lineages reaching far back toward the base of the evolutionary tree. Aquilegia is a member of the basal-most eudicot clade (Ranunculales) and thus is positioned nearly equidistant between the current model systems Arabidopsis and rice. The genus has been used in numerous ecological and evolutionary studies, including speciation due to pollinator shifts, specialization for soil type, mating system evolution, floral development, and adaptive radiation (adaptation of different forms of organisms to different living conditions). The genus is especially well known for its diversity of floral form associated with different pollinators. In addition, nearly all species can be crossed to produce fertile hybrids, making the genetic dissection of this vast diversity possible.

Having the genome sequence for a species representing such a crucial evolutionary node in angiosperm evolution will greatly enhance our understanding of how plant genomes evolve. Furthermore, this sequence will lead to a much deeper understanding of the evolution of morphological, physiological, reproductive, and biochemical innovations found among angiosperms. In addition, Aquilegia offers the opportunity to understand how plants adapt to both biotic and abiotic factors in the environment. Such studies will be especially important for understanding how plants adapt, at the molecular level, to a changing environment such as that resulting from global climate change. For example, A. formosa has a range from Alaska to southern California and spans elevations from sea level to over 10,000 feet, allowing opportunities to study adaptation to different light, temperature, and rainfall extremes. New species of Aquilegia have colonized these different habitats following the major climate changes occurring after the last ice age.

Aquilegia is now poised as an ideal species for whole-genome sequencing. This sequencing will elevate Aquilegia’s status as an attractive model, allowing our collaborators and many newcomers to investigate plant evolution at a new level.

Principal Investigators: Scott A. Hodges (UC Santa Barbara), Justin O. Borevitz (Univ. of Chicago), Elena Kramer (Harvard Univ.), Magnus Nordborg (Univ. of Southern California), and Jeff Tomkins (Clemson Univ.)

拟南芥

Sequencing Arabidopsis lyrata and Capsella rubella, close relatives of Arabidopsis thaliana, will leverage the rich information now available for A. thaliana, arguably the most important reference plant. Arabidopsis lyrata is the closest well-characterized relative in the same genus as A. thaliana, and Capsella is the closest well-characterized genus. Several technologies are currently being used to generate a nearly complete account of intra-species polymorphisms for A. thaliana, a first for any reference organism. The value of this information will be greatly enhanced with information from close relatives.

杨树

Forest trees are the dominant life form in many ecosystems and contain more than 90% of the Earth's terrestrial biomass. Forests throughout the world provide such environmental benefits as carbon sequestration, renewable energy supplies, watershed protection, improved air quality, biodiversity, habitat for endangered species, and access to recreational opportunities. Despite the importance of forest trees for natural ecosystems and the world economy, little is known about their biology in comparison with the detailed information available for crop plants and model organisms such as Arabidopsis. As a result, the forest science community has engaged the resources of the JGI to help sequence Populus trichocarpa, the black cottonwood.

Traditional genetic breeding approaches in forestry are limited by the large size, long generation interval, and out-crossing mating system of most trees. Sequence information will enable forest tree biologists to begin large-scale, thorough analyses of genes and other genetic motifs. This will not only shed light on basic science questions but will also lead to improved plant materials for the forest products industry and ultimately allow selection of novel traits that could be used to address questions related to the energy-related mission of the Department of Energy. Populus (poplar) species are used in activities ranging from carbon sequestration research, to free-air CO2 enrichment (FACE) studies, and to the development of fast-growing trees as a renewable bioenergy resource. The sequencing effort will also inform applications of phytoremediation, where trees can be used to remediate hazardous waste sites.

For more information, see the Populus trichocarpa white paper.

二穗短柄草

The temperate wild grass species Brachypodium distachyon (Brachypodium) is a new model plant for temperate grasses and herbaceous energy crops. Temperate grass species such as wheat, barley, and forage grasses underpin our food supply. However, the size and complexity of their genomes is a major barrier to biotechnological improvement. Similarly, while herbaceous energy crops (especially grasses) are poised to become a major source of renewable energy in the United States, we know very little about the biology of traits that affect their utility for energy production. Thus a tractable temperate grass model is urgently needed to address questions directly relevant both for improving grain crops and forage grasses that are indispensable to our food production systems, and for developing grasses into superior energy crops. Neither rice nor Arabidopsis adequately fits this role.

Brachypodium is closely related to the cool-season grasses and is an emerging model system for the diverse and economically important grain, forage and turf crops that these groups encompass. The small Brachypodium genome can be used as an accurate template for the much larger polyploid genomes of crops such as wheat and barley. Moreover, since Brachypodium is inbreeding, small in stature, can be grown rapidly, and is amenable to transformation it can be used as a functional model to gain the knowledge about basic grass biology necessary to develop superior energy crops. This combination of desirable attributes underlies the burgeoning research interest in the species. A whole-genome shotgun sequence (WGS) of the Brachypodium Bd21 genome, supplemented by a complete set of expressed sequence tags (ESTs), will be a cornerstone resource for a vigorous research community seeking to promote the development of new energy crops and to contribute to global food security.

Principal Investigators: Jeff Chang (Oregon State Univ.), Michael Bevan (John Innes Centre), David Garvin (USDA-ARS), Samuel Hazen (Scripps Research Inst.), Todd Michael (Salk Inst.), Todd Mockler (Oregon State University), and John Vogel (USDA-ARS)

二穗短柄草（Brachypodium distachyon）是一种温带禾草，归属禾本科早熟禾亚科短柄草族短柄草属，具有基因组小、株型小、自花授粉、一年生、生命周期短、有二倍体和一系列多倍体、易培植、易转化等诸多优点，尤其是与很多重要的谷类作物如小麦、大麦、燕麦、玉米、水稻、高梁等以及许多牧草与草坪草有较近的亲缘关系，因而是温带禾本科植物功能基因纽学以及生物能源作物（如柳枝稷）研究的理想模式植物。

 

树薯

Cassava (Manihot esculenta) is an excellent energy source. Its roots contain 20-40% starch that costs 15-30% less to produce per hectare than starch from corn, making it an attractive and strategic source of renewable energy. Cassava grows in diverse environments, from very dry to extremely humid, from acidic to alkaline soils, from sea level to high altitudes, and in nutrient-poor soil. Moreover, it is grown worldwide as a source of food for approximately 1 billion people, raising the possibility that it could be used globally to alleviate dependence on fossil fuels. The effort to sequence the cassava genome will be aided by alignments to the genomes of poplar and castor bean, plants closely related to cassava, and available cassava BAC libraries and EST and cDNA sequences will facilitate annotation. This project will elucidate the genetic machinery required for efficient energy production in a range of environments, and the information it yields will enable improvement to a wide range of crops important for the US biofuel supply.

Principal Investigator: Claude M. Fauquet (Donald Danforth Plant Science Ctr.)

松树

Conifers represent an ancient and diverse branch in higher plant evolution. Some conifer species dominate modern-day ecosystems that are repositories for large amounts of terrestrial sequestered carbon, while others exist in populations numbering tens of individuals. Conifer forests are among the most productive in terms of annual lignocellulosic biomass generation, and coniferous trees are the preferred feedstock for much of the forest products industry, one of the most energy-intensive manufacturing sectors of the U.S. economy. Breeding programs to improve conifers have been in existence for more than 50 years, but progress has been slow because of the large size of the trees and their generally slow progress to sexual maturity.

Climate change and exotic forest pests are threatening certain conifer populations, but a general dearth of genomic resources and tools limits our capacity to address many of these issues and problems. One of the challenges of conifer genomics is that conifers do not have small genomes. Loblolly pine, for example, has a genome roughly seven times the size of the human genome. Thus, complete sequencing of the pine genome is unlikely until such time as sequencing and assembly costs are greatly reduced. Expressed sequence tags (ESTs), which represent the actively expressed portion of conifer genomes, are the most cost-effective route to identify the genes underpinning conifer growth, development, and response to the environment.

The proposed work will more than triple the number of publicly available ESTs for loblolly pine, the species currently serving as the primary reference species for conifer genomics. ESTs will also be generated for 22 other species, some of which have breeding programs and are of economic importance, but many of which have no existing genomic resources. New EST resources will be of immediate use in development of single-nucleotide polymorphism markers for ongoing association genetics studies and breeding for biomass accumulation, as well as for the development of improved oligonucleotide microarrays for functional genomics work. Comparative genomics studies performed using new sequences from previously unstudied conifers will facilitate phylogenetic analyses and greatly improve our understanding of higher plant evolution.

Principal Investigators: Jeffrey Dean (Univ. of Georgia), Glenn T. Howe (Oregon State Univ.), Kathleen D. Jermstad (U.S. Forest Service), David B. Neale and Deborah L. Rogers (Univ. of California, Davis)

 

棉花

The Gossypium (cotton) genus presents a novel opportunity to advance our understanding of the natural world and organic evolution, while nurturing bio-based carbon sequestration alternatives to petrochemical use and improving the sustainability of crop production. The genus has spawned one of the world’s most important crops (cotton), which sustains one of the world’s largest industries (textiles). The value of cotton fiber grown in the USA is typically about $6 billion/yr. Cottonseed oil and meal byproducts add $500 million/yr. More than 440,000 domestic jobs are related to cotton production and processing, with an aggregate influence of about $120 billion/yr on the US gross domestic product and estimated $500 billion/yr worldwide. Increasing the durability and strength of cotton fiber offers the opportunity to replace synthetic fibers requiring more than 200 million barrels of petroleum per year to produce in the USA alone, also increasing use of bio-based products and increasing farm income. Its seed oil, and also byproducts of cotton processing, are potential biofuels.

Cotton evolution involved a fascinating series of events that offer scientists the opportunity to dissect the evolution of a novel organ, the ‘lint fiber’, and also to unravel the consequences of polyploidy, both for the generation of biodiversity and for crop productivity. Gossypium is also ideal for ‘phylogenetic shadowing’ of the Brassicales (including Arabidopsis and Capsella), discerning otherwise cryptic genomic features such as conserved noncoding sequences. Cotton fibers, which can be produced in vitro, represent an excellent single-celled genomics platform that will accelerate the study of gene function, building on a distinguished history of seminal contributions to plant molecular biology. In particular, this may provide unique insights into cellulose biosynthesis that are fundamental to bioenergy (bioethanol) production.

Principal Investigator: Andrew H. Paterson (Univ. of Georgia)

Cotton is one of the world’s most important crops, and it sustains one of the world’s largest industries (textiles). The value of cotton fiber and byproducts grown in the USA is typically about $6-7 billion/yr. More than 440,000 domestic jobs are related to cotton processing, with an aggregate influence of ~$120 billion/yr on the US gross domestic product and ~$500 billion/yr worldwide. Increased durability and strength of cotton fiber offers the opportunity to replace synthetic fibers that require more than 200 million barrels of petroleum per year to produce in the USA alone, also increasing use of bio-based products and increasing farm income. Its seed oil, and also byproducts of cotton processing, are potential raw materials for production of biofuels. The unique structure of the cotton fiber makes it useful in bioremediation, and accelerated cotton improvement also promises to reduce pesticide and water use.

Cotton fibers, which can be produced in vitro, represent an excellent single-celled genomics platform, building on a distinguished history of seminal contributions to molecular biology by accelerating the study of gene function, particularly regarding cellulose biosynthesis that is fundamental to bioenergy production. A genome sequence for Gossypium will facilitate ‘phylogenetic shadowing’ of the Brassicales (including Arabidopsis and Capsella), enabling discovery of otherwise cryptic genomic features such as conserved non-coding sequences. Sequencing under this proposal will augment the JGI's 2006 CSP pilot sequencing of Gossypium raimondii, selected by the worldwide cotton community as the first cotton genotype to be fully sequenced. The United Nations declaration of 2009 as the International Year of Natural Fibers makes this project particularly timely.

Principal Investigators: Andrew H. Paterson (Univ. of Georgia)

浮萍

The Lemnaceae, commonly known as duckweeds, are the smallest, fastest growing and simplest of flowering plants. Some of the current uses of Lemnaceae are a testimony to its utility: basic research and evolutionary model system, toxicity testing organism, biotech protein factory, wastewater remediator, high-protein animal feed, and carbon cycling participant. Sequencing of the Greater Duckweed, Spirodela polyrhiza (L.) Schleiden, which has a genome size similar to that of Arabidopsis (150 MB), will address challenges in alternative energy, bioremediation, and global carbon cycling.

Duckweed photo courtesy Todd Michael.

With the passage of the 2005 Federal Energy legislation, the drive to develop sustainable feedstocks and processing protocols for biofuel production has intensified. The search for new biomass species has revealed the potential of Lemnaceae species. These plants produce biomass faster than any other flowering plant. The carbohydrate content of the plant material also indicates a potential for ethanol production. Moreover, the carbohydrate in duckweed biomass is readily converted to fermentable sugars by using commercially available enzymes developed for corn-based ethanol production.

The utility of Lemnaceae species for bioremediation has long been recognized as well. Propagated on agricultural and municipal wastewater, Spirodela and related species efficiently extract excess nitrogen and phosphate pollutants. Duckweed growth on ponds effectively reduces algal growth (by shading), coliform bacterial counts, suspended solids, evaporation, biological oxygen demand, and mosquito larvae while maintaining pH, concentrating heavy metals, sequestering or degrading halogenated organic and phenolic compounds, and encouraging the growth of other aquatic animals such as frogs and fowl.

A better understanding of Lemnaceae species could also reveal the potential for their role in the global carbon cycle. Primitive aquatic plants have been implicated as the primary source of carbon sequestration that drove global climate change during the Early Eocene. The S. polyrhiza genome sequence could unlock the remarkable potential of a rapidly growing aquatic plant for carbon sequestration, carbon cycling, and biofuel production.

Principal Investigators: Todd P. Michael, Randall Kerstetter, and Joachim Messing (Rutgers); John Shanklin and Jorg Schwender (Brookhaven Natl. Lab.), Elias Landolt (Institut f?egrative Biologie, Switzerland), Klaus Appenroth (Univ. of Jena, Germany), Tokitaka Oyama (Kyoto Univ.), Todd Mockler (Oregon State Univ.)

桉树

A major challenge for the achievement of a sustainable energy future is our understanding of the molecular basis of superior growth and adaptation in woody plants suitable for biomass production. Eucalyptus species are among the fastest growing woody plants in the world, with mean annual increments up to 100 cubic meter per hectare. Eucalyptus is the most valuable and most widely planted genus of plantation forest trees in the world (ca. 18 million hectares) due to its wide adaptability, extremely fast growth rate, good form, and excellent wood and fiber properties. Eucalyptus is also listed as one of the U.S. Department of Energy’s candidate biomass energy crops. Genome sequencing is essential for understanding the basis of its superior properties and to extend these attributes to other species. Genomics will also allow us to adapt Eucalyptus trees for green energy production in regions (such as the Southeastern USA) where it cannot currently be grown. The unique evolutionary history, keystone ecological status, and adaptation to marginal sites make Eucalyptus an excellent focus for expanding our knowledge of the evolution and adaptive biology of perennial plants.

Principal Investigators: Zander Myburg (Univ. of Pretoria), Dario Grattapaglia (EMBRAPA and Catholic Univ. of Brasilia), and Jerry Tuskan (Oak Ridge Natl. Lab.)

猴子花

One of the challenges of 21st-century biology is to determine, at the DNA sequence level, the basis of adaptive evolution in nature. The flowering plant genus Mimulus (monkey flowers) has become a leading model system for studying ecological and evolutionary genetics in nature. JGI will sequence the species Mimulus guttatus.

Since Darwin, Mimulus species have been used to investigate a wide range of topics of interest to ecologists and evolutionarybiologists, including plant adaptation to soils contaminated with heavy metals, mating system evolution, the genetic basis of inbreeding depression, plant/herbivore interactions, adaptive radiation of floral form, life history evolution, and the origin of new species. Compared to other plants whose genomes have been sequenced, Mimulus is uniquely suited for ecological and evolutionary studies because of its tremendous range of floral morphology (and associated pollinators), mating systems (selfing to outcrossing), growth forms (annual herbs to perennial woody shrubs), and habitat preference (desert to riparian to aquatic). A well-resolved phylogeny of the roughly 160 Mimulus species reveals that the genus has undergone two large adaptive radiations, one in western North America and an independent radiation in Australia.

Like all plant genetic model systems, Mimulus species have a small genome (about 430 Mb), a short generation time (6 to 12 weeks), high fecundity (100 to 2000 seeds per pollination), self-compatibility, and ease of greenhouse propagation. Unlike most plant genetic model systems, the ecology of Mimulus is known in great detail, and nearly all studies of Mimulus have a prominent field-based component. Recognizing the need to develop a basic set of genomics tools for an ecologically important model system, the National Science Foundation Frontiers in Intergrative Biological Research program has funded a $5 million, 5-year integrated ecological and genomic analysis of the genomes of M. guttatus, M. nasutus, M. lewisii, and M. cardinalis. The Mimulus genome sequence will complete the genomics toolkit.

CSP project participants: John H. Willis (proposer) and Fred Dietrich (Duke Univ.), Toby Bradshaw (Univ. of Washington), Lila Fishman (Univ. of Montana), Douglas W. Schemske (Michigan State Univ.), Jeffery P. Tomkins (Clemson Univ.), Todd Vision (Univ. of North Carolina), and Paul Beardsley (Idaho State Univ.).

 

高梁

One of the world’s leading grain crops, sorghum is also an important model for tropical grasses of worldwide importance with a collective minimum economic impact of $69 billion U.S. per year. As a model for the tropical grasses, sorghum is a logical complement to Oryza (rice), the first monocot plant to be sequenced. Sorghum is representative of the tropical grasses in that it has "C4" photosynthesis, using a complex combination of biochemical and morphological specializations resulting in more efficient carbon assimilation at high temperatures. By contrast, rice is more representative of temperate grasses, using "C3" photosynthesis.

In addition to its intrinsic value, the sorghum sequence will be a valuable reference for assembling and analyzing the fourfold larger genome of maize (corn), a tropical grass that is the leading U.S. fuel ethanol crop (sorghum is second). Sorghum is an even closer relative of sugarcane, arguably the most important biomass/biofuels crop worldwide with annual production of about 140 million metric tons and a net value of about $30 billion. Sorghum and sugarcane are thought to have shared a common ancestor about 5 million years ago. The two have retained largely common gene order, and some genotypes can still be intercrossed. However, sugarcane has undergone at least two cycles of whole-genome duplication, resulting in a genome larger than that of human and with four- or higher-fold redundancy of most genes. By contrast, sorghum is diploid with a genome about 25% the size of human, maize, or sugarcane.

The Sorghum genus is also noteworthy in that it includes one of the world’s most noxious weeds. The same features that make "Johnson grass" (Sorghum halepense) such a troublesome weed are actually desirable in many forage, turf, and biomass crops that are genetically complex. Therefore, sorghum offers novel learning opportunities relevant to weed biology as well as to improvement of a wide range of other forage, turf, and biomass crops.

Sorghum genome early release data is available via Phytozome.

CSP project participants: Andrew H. Paterson (proposer), John E. Bowers, and Alan R. Gingle (Univ. of Georgia); C. Thomas Hash (Int'l Crops Research Inst. for the Semi-Arid Tropics); Stephen E. Kresovich (Cornell Univ.); Joachim Messing (Rutgers); Daniel G. Peterson (Mississippi State Univ.); and Daniel S. Rokhsar (JGI and UC Berkeley).

柳枝稷

A long-standing mission of the DOE has been to develop alternative sources of energy from biomass, and with good reason President George W. Bush specifically mentioned switchgrass as a promising energy crop in his 2006 State of the Union Address. This native grass has many traits that make it well suited for use as an energy feedstock. Yields of switchgrass are high, averaging 7 tons per acre in unirrigated field trials with some lines yielding up to 10 tons per acre. Production costs are low because of the plant's low nutrient use, minimal pesticide requirements, propagation by seed, and perennial growth habit. Switchgrass can be harvested with conventional haying equipment, and its wide adaptability allows it to be grown productively across a large geographic area, including marginal regions that would otherwise be unproductive. Associated environmental benefits of switchgrass cultivation derive from its large root mass, which increases soil organic matter, prevents soil erosion, and acts as a carbon sink, further sequestering greenhouse gases. It is currently planted on much of the 32 million acres of land that has been enrolled in the USDA Conservation Reserve Program, and continuing work within the USDA, DOE, and scientific community is focusing on production methods, cultivar improvement, and feedstock quality.

Through the generation of a large number of expressed sequence tags (ESTs), this sequencing effort will likely identify most genes in switchgrass and also will uncover a large segment of the molecular diversity in this species. This diversity is likely to include allelic variation in genes contributing to biomass production and other traits relating to its properties as a feedstock. As an undomesticated species in a relatively low-input production system, the most practical approach to improving biomass yield potential in switchgrass is through release of improved cultivars. Exploitation of this large data set will hasten development of DNA marker-based molecular breeding approaches that will speed the process of cultivar development by allowing artificial selection at the seedling stage. The EST data will also enable basic genetic and physiological studies focused on feedstock improvement by providing an inventory of genes that can be studied.

Principal Investigators: Christian M. Tobias and Gautam Sarath (USDA-ARS).

甜橙

Sweet orange (Citrus sinensis L.) is one of the most important fruit crops in the world. Although considerable genetic diversity is available within the genus, diversity within Citrus sinensis is quite limited as all known cultivars have originated by mutation, not by sexual hybridization. Citrus breeding by conventional means, in general, is hampered by a long generation time, high heterozygosity, inability to produce inbred lines, and apomixis in many important cultivars. Sweet orange is a diploid species, with 9 pairs of chromosomes and a small genome size (382 Mb). It is placed in the Sapindales, a sister taxon to the Brassicales which contains Arabidopsis, but is otherwise taxonomically isolated from other plants with genome sequencing projects. Genome sequencing will complement other citrus genomics resources now available or under development, including a considerable EST database, high density microarrays, a BAC physical map, and a high density linkage map. These tools will allow geneticists and breeders to more effectively manipulate various traits in breeding programs. A genome sequence for Citrus will also facilitate comparative genomics research by expanding genome sequence data to a new taxonomic group, and should be particularly valuable for comparative studies with poplar and other trees

Pineapple orange

The initial JGI project will provide low sequence coverage (about 1.2 X) of ‘Ridge Pineapple’ orange, using a combination of plasmid and fosmid clones. JGI will also sequence about 4000 cDNA clones to obtain 3' ends of genes currently lacking this information. To assess the accuracy of sequence assembly in six heterozygous regions, 24 BAC clones that were assigned to haplotypes using SSR markers will be sequenced and assembled. It is hoped that the initial project will provide a foundation for a full genome sequence in the near future

Principal investigators: Mikeal L. Roose and Timothy J. Close (UC Riverside), Randy Niedz (USDA-USHRL), Abhaya Dandekar (UC Davis), and Fred G. Gmitter Jr. (Univ. of Florida).

大豆

Soybean (Glycine max) is the most valuable legume crop, with numerous nutritional and industrial uses because of its unique seed chemical position. The soybean seed is the world’s main source of vegetable protein and oil, accounting for over 55% of all oilseed production and 80% of the edible consumption of fats and oils in the US. Industrial applications of soybean oil include lubricants, emulsifiers, coatings, and biodiesel. Over 3.1 billion bushels of soybeans were produced in the US on nearly 75 million acres in 2004, with an estimated annual economic value exceeding $16 billion, second only to maize and approximately twice that of wheat and ten times that of rice (as reported by the National Agricultural Statistics Service).

Soybean is the principal source of biodiesel (methyl soyate), a renewable, alternative fuel produced by combining soybean oil with methanol. Biodiesel has the highest BTU (energy content) of any alternative fuel. Biodiesel is also significantly more environmentally friendly than comparable petroleum based fuels, since it degrades as rapidly in the environment as sugar and is tenfold less toxic than salt. It also burns more cleanly than conventional fuels, releasing half of the priority pollutants (e.g., carbon monoxide, sulfates, particulate matter, etc.), and reducing the production of carcinogenic compounds (e.g., polycyclic aromatic hydrocarbons) by more than 80% (Plant Physiol. 135: 59-70). As an alternative fuel, biodiesel compares favorably with ethanol production from corn, since soybean requires no nitrogen fertilizer due to its ability to capture nitrogen from the air through the root symbiosis with nitrogen fixing bacteria. Biodiesel is registered as a fuel and fuel additive with the EPA and meets clean diesel standards established by the California Air Resources Board (CARB); the Congressional Budget Office and the US Department of Agriculture have certified biodiesel as the lowest cost alternative fuel option for meeting the Environmental Policy Act standard. Enhancements in domestic biodiesel production have the potential to alleviate US dependence on petroleum.

You can learn more about biodiesel at the National Biodiesel Board's web site. The Missouri Soybean Association site has more information about soybeans.

Principal investigators: Gary Stacey (Natl. Ctr. for Soybean Biotechnology, Univ. of Missouri), Randy Shoemaker (USDA Agricultural Research Service), Scott Jackson (Purdue Univ.), Bill Beavis (Natl. Center for Genome Resources), Daniel Rokhsar (DOE-JGI).

石松 卷柏

The lycophytes are an ancient lineage of vascular plants that arose about 400 million years ago. Lacking true leaves and roots, they are a key node of the plant evolutionary tree. The nuclear genome content of the lycophyte Selaginella moellendorffii (65-88Mbp) has the smallest genome size reported for a land plant species, about two-thirds that of Arabidopsis thaliana. A draft sequence of the S. moellendorffii genome will be useful to the plant biology community in many ways. First, as a clade intermediate between nonvascular plants (the algae and bryophytes) and all other vascular plants, it will serve as a reference genome for bridging large-scale genome comparisons. Having a compact genome, its sequence will be useful for cloning genes, annotating other genomes, discovering new genes, predicting regulatory regions of plant genomes, and constructing rooted and accurate gene and phylogenetic trees. Its sequence will also be a welcome resource for researchers interested in testing theories of plant evolution, particularly those relating to the evolution of traits fundamental to vascular plants, such as vascular tissue and lignification, root/stem/leaf organography, complex patterns of sporophyte branching, and the elaboration of reproductive structures, such as flowers, fruits, and seeds. Finally, its compact genome will help to define an ancient core of genes that are common to all vascular plants.

CSP project participants: Jo Ann Banks (proposer), Clint Chapple, Scott Jackson, Joe Ogas, Robert Pruitt, David Salt, and Dan Szymanski (Purdue Univ.); John Bowman and Sandra Floyd (Univ. of California, Davis); John Carlson, Dan Cosgrove, Claude dePamphilis, and Hong Ma (Pennsylvania State Univ.); Ned Friedman (Univ. of Colorado); and Dina Mandoli (Univ. of Washington).

Loblolly pine (Pinus taeda L.) is an organism of tremendous economic and ecological
importance and a key representative of the conifers, an ancient lineage of plants that dominates many of the world’s temperate and boreal ecosystems. Loblolly pine’s fast growth, amenability to intensive tree farming, and high-quality lumber/pulp have made it the cornerstone of the U.S. forest products industry and the most commonly planted tree species in America; approximately 75% of all seedlings planted each year are loblolly pines. Its ability to efficiently convert CO₂ into biomass and its widespread use as a plantation tree have also made loblolly pine a cost-effective feedstock for lignocellulosic ethanol production and a promising tool in efforts to curb greenhouse gas levels via carbon sequestration. Despite the importance of loblolly pine and other conifers, genomic sequence information for this taxon is extremely limited. EST resources are available as a result of sequencing efforts at JGI and elsewhere, but actual genomic DNA sequence data is needed to enable efficient tree improvement. JGI plans to sequence 100 clones from an existing BAC library. Of these clones, 50 will be selected based upon the presence of genes involved in carbon metabolism and/or wood formation, 25 will be chosen based on low repeat content, and 25 will be picked at random. BAC sequencing will provide unprecedented insight into genome organization in loblolly pine and conifers in general.

Principal Investigators: Daniel G. Peterson (Mississippi State Univ.), Jeffrey F.D. Dean (Univ. of Georgia), C. Dana Nelson (USDA Forest Service), Ronald R. Sederoff (North Carolina

叶苔

The origin of land plants (embryophytes) was one of the major evolutionary events in the history of planet earth. Experimental, paleontological, morphological, and molecular systematic data all point to the liverworts as being some of the first plants to evolve and colonize the Ordovician landscape. Thus liverworts are a key group to include in any comparative study aimed at understanding the origin and evolution of organisms that now cover much of terrestrial earth. Marchantia polymorpha is a common, easily cultivated liverwort that exhibits many primitive characteristics of both liverworts and land plants. M. polymorpha has been widely studied by researchers in physiology, anatomy, and genetics and is included as the exemplar in most phylogenetic analyses of land plants.

The M. polymorpha genome sequence will be useful in several ways. The recent sequencing of Selaginella moellendorffii and Physcomitrella patens genomes has already made genomic comparisons at deeper phylogenetic levels possible. Since liverworts have convincingly been resolved as the sister group to all other land plants, the addition of a liverwort genome will allow genomic comparisons that span the breadth of extant embryophyte diversity. The ability to compare genomes of a liverwort, a moss, a lycophyte, and several flowering plants will provide critical insight into the similarities and differences in developmental, structural, and physiological genes in plants with strikingly different morphologies and life histories.

Combining access to a sequenced genome with techniques being developed to study and manipulate genes in M. polymorpha will allow this plant to become a model organism for understanding the genetics of development in a plant that may be as close a living example as possible of what an ancient land plant might have been, making it possible to identify the suite of genes that are common to all land plants. As a representative genome from the sister lineage to all other land plants, the genome of M. polymorpha will be as significant for understanding land plant evolution as the genomes from the choanoflagellate Monosiga brevicollis and the lancelet Branchiostoma floridae (both recently released by the JGI) are to understanding evolution of the metazoan and vertebrate clades.

Principal Investigator: John Bowman and Sandra K. Floyd (Monash Univ.), Takayuki Kohchi and Hideya Fukuzawa (Kyoto Univ.), and Kanji Ohyama (Ishikawa Prefectural Univ.)

 

 

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